MolNFT v1 · #146055 · protein
Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed ar protein OFF7
6D65 · Maltose-binding periplasmic PROTEIN,DUAL specificity…: “Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding…”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability…
- PDB
- 6D65
- Type
- protein
- Length
- 1,333 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,DUAL specificity protein phosphatase 1; Designed ar…
- EC
- 3.1.3.16, 3.1.3.48
- UniProt
- P0AEX9, P28562
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,DUAL specificity protein phosphatase 1 (EC 3.1.3.16, 3.1.3.48) | protein | 511 | 45% helix, 20% strand | P0AEX9, P28562 |
| B | Designed ar protein OFF7 | protein | 155 | 54% helix, 0% strand | — |
| C | Maltose-binding periplasmic PROTEIN,DUAL specificity protein phosphatase 1 (EC 3.1.3.16, 3.1.3.48) | protein | 511 | 45% helix, 20% strand | P0AEX9, P28562 |
| D | Designed ar protein OFF7 | protein | 156 | 54% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 23 copies · chains A, D, B, C
- EOH · Ethanol · additive · 21 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.63 | 0.78 | 37 | GOL |
| 2 | 314 | 0.61 | 0.79 | 41 | EOH |
| 3 | 318 | 0.61 | 0.78 | 49 | EOH |
| 4 | 353 | 0.61 | 0.77 | 39 | SO4 |
| 5 | 270 | 0.55 | 0.76 | 33 | empty |
Interfaces
5 interfaces between chains.
- C–D · 723 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 318 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 298 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6D65 · Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as… · the same entry in another collection · chain A against A, TM-score 1.00
- P28562 · AlphaFold monomer V2.0 prediction for dual specificity protein phosphatase 1 (P28562) · a predicted model of the same protein · chain C against A, TM-score 0.30
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0AEX9
- Every structure of UniProt P28562
- Elsewhere: RCSB PDB 6D65 · PDBe 6D65 · UniProt P0AEX9 · UniProt P28562
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